A Glitch in the System
by MileRun
Summary: Whose story is it? A boy who finds a rare Pokemon in the wild? A scientist who found Pokemon the world had never seen? A liar stuck in an unwanted form? A young woman who never wanted to fight? Or is this a story of a Pokemon critical to all their goals?
1. Prologue G

**_Disclaimer_**: I do not own intellectual rights to Pokémon, nor do I ever plan on claiming intellectual rights to Pokémon or making money off of the Pokémon franchise unless I somehow in the distant future do manage to earn intellectual rights to Pokémon, which is extremely unlikely. This story is written without the slightest thought of profit in mind and is published to be hosted on for anyone to see free of charge.

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****Prologue: Project Jailbreak**

The alarm rang just shortly after the sun rose. It was going to be an exciting day for Glitch. Without a second thought, Glitch hopped out of bed and sped off to greet Professor Fir.

The alarm was still buzzing when Glitch entered Fir's room, but the professor was still fast asleep. Just like Fir had trained him, Glitch let loose a mild Thunderbolt. Professor Fir jumped awake. "Ampere, I swe- huh?" The elderly scientist looked around and found himself safely in his room. Looking to the ground, the retired professor caught sight of his only remaining Pokémon expressing happiness and eagerness as best as it could.

"Good morning, Glitch!" Professor Fir shouted with a large smile on his face. "Quite a nightmare I had there. Silly little thing, too, hahaha! Come on, let's get some breakfast!"

Glitch, of course, did not need to eat. It also did not have to drink, sleep, or breathe. Glitch was a standard, run-of-the-mill Porygon, if not a slightly outdated model. Nevertheless, the professor had made a habit of putting out a bowl of Pokémon food for Glitch while he ate, as he did for all the Pokémon he had during the glory years.

The professor enjoyed thinking back to the good times he'd enjoyed with his friends: Ampere the Electrode, who had evolved from his prized starter; Yarly the Noctowl, who had evolved from his first capture; Turret the Octillery; Compound the Muk; Pharaoh the Dusclops, for whom Fir never could find a Reaper Cloth; and, of course, Amber, the Aerodactyl that Professor Fir had "revived" on his own.

They had undergone many adventures together, earned badges from across the world, and maybe – "unofficially, of course," the professor added to his thought – had encounters with Pokémon the human world isn't ready for. Glitch joined the family shortly after Ampere passed away. The professor painstakingly programmed the Porygon himself. But that was all in the past. Today, it was just Glitch and the retired professor, and today would be an exciting day for the both of them. The thing is, neither one knew just how exciting it would be.

A gentle knock on the door shook Professor Fir from his thoughts. He got up from his seat and ran downstairs with the normal cheerful bounce in his step, Glitch sliding along closely behind him. Waiting patiently at the door, without so much as knocking a second time, was a young, twenty-something woman in a formal black dress.

"Good morning, professor," she spoke as he opened the door. Her voice was strong, the professor observed, but at the same time, gentle, almost solemn.

"Please, call me Simon. It's been years since I've done anything worthy of the title 'Professor.' What may I do for you, Miss…?"

"Woodwind, sir. I was doing some research, and I was hoping to speak with you about a project you had worked on a few decades ago."

"Please, come in." The professor gestured to his living room. "Glitch, could you fetch some coffee for Miss Woodwind?" Glitch nodded and glided back away. The professor and his guest were still within earshot.

"Well, Miss Woodwind, I'm flattered that you would come here, but most of my research can be found in your local library."

"I'm actually here about your last project: Project Jailbreak."

"Ah, Project Jailbreak. I'm not sure how you learned of that, but you do understand that it is classified, correct?"

Their voices trailed off as Glitch entered the kitchen. Raiding the pantry, Glitch found a nearly-empty case of instant coffee and poured the last of the sand-like grains into a cup. Before the water had even started to boil, however, Professor Fir and Miss Woodwind were again audible, now moving towards the lab.

"Glitch," the professor called, "Come this way please." Something was odd about his tone. Glitch's audio sensors picked up strange fluctuations in his vocal patterns. To the untrained ear, it would sound like Fir's everyday, cheerful call. Glitch, however, was able to pick up signs that it attributed to sorrow and distress.

Emulating worry to the best of its ability, Glitch followed Fir and Woodwind into the lab and approached the main computer. "Glitch, extract file 372273," Fir said, his façade starting to fail as tears formed in his eyes. Glitch recognized the number as an emergency code – "escape, and do not return." With a flash resembling a bolt of lightning, Glitch converted itself into data and uploaded itself into the computer. It travelled through the network and emerged from a monitor hidden outside the house, an escape route specifically made for the Porygon.

Glitch silently sped away as a gunshot rang from within the lab. Suddenly, Glitch felt something like a jolt of electricity flow through its body. It had experienced this sensation before, but never to this degree; perhaps it was just a bug in Glitch's programming, or something to that effect. Either way, Glitch would describe it, with its limited capacity for emotion, as "unpleasant."

* * *

Glitch had been wandering for some time now. It was now in unfamiliar territory. Porygon are not accustomed to being away from urban areas, let alone roaming in tall grass. Glitch was not even sure why it was out on a route; Fir's final order was for Glitch to leave the house, not to get out of town. Still, something in Glitch's data directed it as far away from the lab as possible.

A burst of sound suddenly rattled Glitch's mind. Disoriented, Glitch spun around and saw the blurry form of a human and a floating eyeball. Before the Porygon could act, a wave of electricity knocked Glitch into the air. Glitch was numb all over, unable to move, barely conscious enough to see. As it struggled to get up, the Pokémon found itself forced to convert its mass into energy. It put up a hopeless struggle, but ultimately did not have the strength to return to material form.

"A Porygon," came a muffled voice, belonging to a boy probably no older than eleven. "These things are rare! The stats look good for its level… And it's Timid, too! This'll do nicely!"

The last sentence faded out, as if Glitch was being moved farther away from the source of the voice. There was the familiar click of a Poké ball being clipped to a belt, and all was silent.

That certainly was an exciting day.

* * *

Author notes:

Thank you for reading. "A Glitch in the System" is the first fic I've ever decided to put online. It is technically the only one I've actually physically written (er, the only one of acceptable quality, that is), since I'm pretty shaky when it comes to writing scenes and dialogue. "A Glitch in the System" is really something more of an "authorship exercise" for me right now, so I apologize in advance if this comes off as shaky or rough. Please leave your honest opinions; even the slightest bit of constructive criticism can help.

I do have the entire story planned out, so not much time will be lost on deciding what should happen next. So, you can expect somewhat frequent updates. In fact, the next one should be posted almost concurrently, though it's not quite a chapter for Glitch's story (see the author notes for that).


	2. Prologue JP

Author's notes:

I don't plan to have notes on every chapter, but I thought they might be rather important here. This second prologue chapter (really a second and third prologue) is for the two subplots that will tie into the main storyline. The inspiration for this setup probably came from reading either Holes or too many Animorphs books when I was younger. Neither of the subplots is _technically_ important to the main story, but since events relating to and/or resulting from both subplots will pop up later in the main story, the subplot chapters will provide background; they're just there so that things don't look like they came out of nowhere.

Anyways, as far as chapter order goes, you can expect a Glitch Journal Glitch Peter Glitch pattern to pop up. Glitch chapters will be marked with "(G)", Journal chapters will be marked with "(J)", and Peter chapters will be marked with "(P)". As mentioned before, I will be updating fairly frequently, so even if you choose just to read the Glitch chapters, you will get your updates at a reasonable pace.

I guarantee that this will be the last prologue chapter, by the way. My next update (tomorrow, perhaps) will start to get into the meat of the story.

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Prologue 2a – Once a Faker, Always a Faker

Why hadn't he just given up? Peter was an adult; he was supposed to be more mature than that! But no, he had to threaten the blasted nerd with a Pokémon battle, and now he's stuck in the wilderness, searching for his first Pokémon.

In his defense, Peter Loki always got away with stuff like this. He was large and intimidating, not to mention rich, and "popular" from kindergarten straight through his current junior year of college. This may very well be the first time anyone ever called a bluff of his. It was due to happen, though; Peter's entire life was basically one large bluff after another.

Stupid Super Nerd, stupid Victreebel, stupid Pokémon in the stupid forest… Peter had spent nearly two hundred thousand coin on assorted Poké balls – a small scratch in his wallet, but annoying nonetheless. With nothing to weaken his targets, though, everything he had gone after was able to break the capsule after a short struggle (because Peter couldn't be bothered to capture worthless Zigzagoon and Taillow, of course), and he was almost out of stock.

Just as he was about to give up, Peter caught sight of a faint light. Moving in as silently as he could, Peter found his way to a small clear. Within, nursing what looked like a particularly nasty leg wound, was something one shouldn't even be able to find in the wild: A Ninetales! If he could catch this and show it off back on campus, he could possibly scare that nerd away without a fight!

Clutching his last Ultra Ball tightly, Peter flung it with all his strength at the serene fox, striking it cleanly in the ribs and trapping it in an instant. Peter ran to the ball while the Ninetales struggled within. In a large blast of flame, the Ninetales exploded out of the capsule while Peter was no more than a yard and a half away. Unwilling to give up, Peter lunged at the impeded fox, wrestling it to the ground. Even in its wounded state, the Ninetales broke free of his grasp with ease and grace.

Then came the crucial mistake. Wildly flailing his arms, Peter caught hold of one of the retreating fox's tails.

The change in atmosphere was immediate. Peter released his grip out of fear, but it was too late. Ninetales, eyes glowing in rage, turned to face her violator. Walls of blue flame erupted from the ground, balls of fire hung in the air, and yet, to Peter, everything felt so cold.

"P-please! I didn't-"

"_Silence!_" commanded the Ninetales. Peter couldn't tell if she was speaking or communicating telepathically, but frankly, that wasn't Peter's largest concern at the moment. "How _dare_ you tarnish my fur with your filthy hands!?"

"I… Oh, did I do th… I didn't mean-" Peter was interrupted again.

"Don't try to defend yourself. I can see the very recesses of your mind. I know everything that you are, everything that you have done, and everything you were planning to do." Peter gulped. He tried to back away, but his fear was wholly immobilizing.

Ninetales continued. "You have always thought yourself to be superior to nature; you will now spend the rest of your life trying to blend in. You have always thought yourself a superior human; you will now be at the mercy of your kin. All you claim is fake; forever shall you be a faker and an imitator. For a thousand years, you shall be burdened by this curse!"

Peter felt himself shrinking. His flesh was hardening into stone. His whole body was in pain as he violently mutated, but into what? There was a hospital in town… Perhaps, if he got to it in time, they could do something! He ran as fast as his increasingly stubby legs could take him, but time was already up.

"Run all you want! You are no longer a man! But then again, you never were."

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Prologue 2b – Cue the Music

It was a small gathering, but the meeting's importance could be felt in the air. A tall, slender man in a lab coat and two large, muscular men wearing strange-looking jumpsuits stood along the wall. At the center of the room was a skeletal-looking man sitting in a large chair, though his pitch-black clothing and the dim light made it difficult to tell where the man and the chair met. Perched on his left armrest was a Chatot, and a Kricketune sat on the right. All in the room had ghostly-white S's somewhere on their uniforms except for one – a woman, standing before the sitting man, who was still garbed in a formal, black dress.

"He was going to activate the laboratory's defense systems. I had no choice but to neutralize him. It won't matter in the long run, anyways." Her boss was buying every word, much to Brass' annoyance. He had brought Woodwind to the conductor expecting some form of punishment for killing the man she was sent to recruit. She'd had her way for too long, and she's still having her way now.

"What's done is done," said the conductor, officially letting Woodwind off the hook. She was one of the founding members of the organization, after all. "Did you find anything of importance?"

"The Rotom you provided for me thoroughly searched every computer and data storage device in the house and lab. The documents were nowhere to be found. But, the visit was not a complete waste." Woodwind paused to produce a small package. "We were able to retrieve Professor Fir's written journal. It may provide clues as to where the documents are stored."

"That could prove vital," the conductor said with a hint of excitement in his voice. "Strings, have one of your researchers read through the journal very carefully and alert me immediately if you find anything. Percussion, send your grunts to all of the late professor's known labs. Brass, Woodwind, you are dismissed."

The man in the lab coat left with the journal, while the smaller of the two muscular men left speaking into a walkie-talkie. The larger man and the woman walked together out the same door, each watching the other carefully. The skeletal-looking man remained in the room with his Pokémon. Deep in the back of his mind, even in spite of his excitement, the conductor couldn't help but feel that the journal wouldn't give him what he wanted.


	3. Welcome to the Family G

**_Disclaimer_**: I still don't own Pokémon, I'm still not claiming to own Pokémon, and I'm still not using this story for profit.

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**Welcome to the Family**

"Go, Porygon!"

Glitch emerged in a flash of light in a completely different setting than it remembered. It was now sitting on a platform floating on an indoor pool of water. Before Glitch was a Floatzel and a strange-looking man in a blue Luchador's mask.

"Magnemite weakened it for you," came a voice from behind Glitch. This voice matched that of the child that attacked him a while back. "It's fast, but you should have no trouble taking this out."

"Aqua Jet, now!" the man in the mask ordered. Encased in an aura of water, the Floatzel rammed Glitch hard. Without any time to react, Glitch was carried off of the platform and into the pool.

"Magnet Rise!" the boy shouted. "Magnet Rise! Do it!" Glitch took the child's advice. Surrounding itself in a magnetic field, Glitch lifted itself out of the water.

"Move in for Ice Fang!" Following its master's command, the Floatzel leapt from directly below Glitch with fangs borne.

"The angle's bad…" Glitch's trainer muttered. "Knock it out of the air with Psybeam!" Once again, Glitch obeyed. It was an odd feeling; Glitch wasn't forced to obey, nor did it particularly want to obey, but it simply obeyed. It was neither free will nor mind control that compelled Glitch to fire its Psybeam, but some twisted combination of both. Yarly, Professor Fir's Noctowl, had told Glitch that this was the power of the Poké ball and the gym badge, but even Glitch's high processing power couldn't imagine this sensation until now.

Floatzel hit the surface of the water hard, but it wasn't out yet. "Porygon, do you know any electric attacks?" Glitch's trainer asked. "Spark, Discharge, Thunderbolt..?" Floatzel popped its head out of the water and prepared for the masked man's next command. "If you do," continued the trainer, "use it now!"

Floatzel stream of saltwater hit before Glitch could charge its Thunderbolt. The brine stung at the scrapes left behind from Floatzel's first attack and barely splashed into Glitch's eyes. Firing blindly, Glitch retaliated with a Thunderbolt in Floatzel's general direction. The bolt nicked Floatzel, but the weasel was able to jump onto Glitch's starting platform to avoid the bulk of the blast. Its trainer gave another order. "Brine again!"

"Come on… Porygon, use Conversion 2!" Glitch's color scheme changed to dark blue and sea green. Now a Water-type, Glitch was able to withstand the Water-type attack, although the sting from the saltwater on Glitch's wounds worked did much to nullify the type advantage. Glitch's trainer didn't seem satisfied. "Try Conversion 2 again!" Conversion 2 again? Glitch was hoping that he would call for Recover. What good would changing into another water-resistant type do? Glitch did it anyways, though. There was that odd sensation again, making Glitch obey without actually forcing it to obey. Glitch's dark-blue body turned vibrant green and its sea-green feet, tail, and beak became a floral pink: Glitch was now the Grass-type.

"Bad move, kid!" the masked man shouted. "Floatzel, Ice Fang!"

"Undo your Magnet Rise!" commanded Glitch's trainer. As fast as Floatzel was, gravity was faster. The weasel's teeth barely grazed Glitch as the Porygon plummeted into the pool.

It was only now that Glitch pieced the strategy together. Magnet Rise wasn't just to get Glitch out of the water; it was bait to get Floatzel out of the water. Changing to the Grass-type was bait for the physical Ice Fang, extra insurance that the masked man would order Floatzel to leap into the air. Now, there was nowhere for Floatzel to dodge. Now, there was no way for Floatzel to use its superior speed to its advantage. Now, with Glitch underneath, Floatzel was at Glitch's mercy.

"Fry it!"

Cackling with electricity, Glitch unleashed a powerful Thunderbolt. Unable to ground the blast, sparks of electricity shot out of Floatzel in all directions. The weasel was unconscious before it hit the water. The masked man returned the Floatzel to a Poké ball while offering it a few words of consolation.

"Come back," shouted Glitch's trainer. In a flash of light, Glitch was once again locked within its Poké ball.

* * *

Glitch's next sight was of a Magnemite and a Gastly. The three of them were in a strange area that appeared similar, Glitch noted, to a computer's network. Both the Magnemite and the Gastly appeared to be very relaxed, and within one second, Glitch learned why; a waft of soothing energy hit Glitch, relaxing it and healing its wounds.

"Hello," the Magnemite said to Glitch in a language that only Pokémon could comprehend. "I apologize for attacking you on the route earlier today, but our trainer deemed you worthy for capture and wished for me to weaken you. But, welcome to the team. I was never assigned a name, so please refer to me by my species. Do you have a name?"

"I am called 'Glitch'."

"Yeah, and I'm Wisp," the Gastly impatiently interjected. "So…" Wisp turned to face Magnemite. "Did you win?"

"Pardon?" Magnemite responded.

"We're in a Pokémon Center's recharge machine, so the gym match against Wake is clearly over. I beat Wake's Quagsire with Giga Drain and the Gyarados took me out with a cheap Bite, but your Discharge should've handled it," said Wisp.

"I beat the Gyarados but lost to Floatzel's Brine. Glitch did not seem to have much physical damage when he was loaded into the recharge machine." Wisp and Magnemite both turned and stared at Glitch.

Glitch spoke up. "I did defeat the Floatzel, if that is what you are asking."

"Ha HA! Take that, Faust!" Wisp roared in laughter.

"That was Wisp's old trainer," Magnemite noted, sensing Glitch's confusion. "He and Wisp started together in Solaceon town, but-"

"But that fickle jerk traded me for an Electabuzz when he couldn't beat Wake on his first try," interrupted Wisp. "An Electabuzz that our new trainer caught in about half an hour! Faust'd better hope that he doesn't run into me again, because Curse works on more than just Pokémon!"

"Our new trainer… Pardon me, but what is our new trainer's name?"

Wisp fell silent. It seemed like Wisp only now realized that he didn't know his own trainer's name. Magnemite answered Glitch's question.

"His name is Michael Orpheus. Michael and I departed together from Sunyshore City the day before yesterday. Sunyshore's gym takes in School Kids with Pokémon and trains them against gym challengers. Michael and I began training at the gym approximately one year ago." Magnemite stopped. Glitch could feel the healing energy of the recharge machine wane. "But," Magnemite continued, "it looks like I will have to share our story some other time."

"Aw, it's over already?" Wisp complained as he vanished in a flash of light.

"I hope to see you again soon," Magnemite said while it disappeared in another flash.

A third flash came and pulled Glitch out of the machine.

* * *

With just a single Thunderbolt, the wild Chatot fell to the ground unconscious. Before that, it had been a Wingull. They had felled at least two Shellos before that, and Glitch didn't even know what Wisp and Magnemite had been fighting. As Michael traveled east back to Sunyshore, for a reason that he didn't think to disclose to his Pokémon, he used Glitch and the others to plow through any wild Pokémon that popped up in the tall grass. Glitch didn't like this practice at first, but this was standard training for captured Pokémon and their captors, and Glitch did genuinely feel as though it was getting stronger after every fight. Anyways, it wasn't as though like Glitch could disobey Michael's orders, and if Glitch was worn down enough, Michael would bring it to the Pokémon Center, where it could meet with Wisp and Magnemite again.

Somewhere along Route 222, Michael decided to just leave Glitch out of the ball for convenience, since Glitch needed the most training anyways. This was Glitch's first chance to get a good look at the trainer. He was dressed plainly in khakis and a white winter jacket with a folded-wing graphic on the back and a lyre design over the chest. With Glitch trailing behind except when in battle, however, the Porygon never found an opportunity to make eye contact with its trainer. Actually, since Glitch's eyes were only about two-and-a-half feet off the ground, Glitch had difficulty making out Michael's facial features in general. If Michael was to change his clothes, Glitch might not be able to recognize him.

Leaving behind a trail of unconscious Pokémon, Glitch and Michael finally reached Sunyshore and arrived at what was presumably Michael's house.

"Mom, I'm home!" Michael announced as he entered. Glitch glided closely behind.

"Welcome back, honey! How was the trip? Did you get your badge?"

"Of course, mom! All it took was a little bit of strategy," Michael responded. Changing tone, he continued: "You know, I won't be able to come home all the time after I get past Veilstone."

"I'm just glad you're home now." She caught a glimpse of Glitch. "Oh, you have a new pet!"

"Mom!" Michael blushed. "They're only pets if you keep them around the house just to look at, or something. These are only for battle."

"Whatever you say, sweetie. Speaking of pets, dad's Delibird dropped off a package for you. I left it in your room."

"Great! Porygon, come here!" Glitch followed Michael as he ran into a tidy bedroom. When Glitch arrived, Michael had already opened the box and removed several discs from within.

"TM13, another TM13, TM15, TM22, TM24, TM29, another TM29, and TM30 – everything I asked for. And this," he added, extracting a blue rock from the package, "will be our secret weapon against Maylene. "Let's get these TMs onto you right away. Porygon, return!"

* * *

Author's notes:  
Okay, so I kinda' lied. This is _basically _another prologue chapter, this time to paint a picture of Michael, but hopefully, there was enough action to balance out the exposition. Anyways, I've been having computer problems, so I'm behind schedule on writing by a few days. Unless the problems persist, I'll be using this week to catch up. Sorry for the delay. The next chapter is a journal chapter, a look at Prof. Fir's past investigations that pave the way for events that happen in the Glitch storyline. If all goes well, expect it tomorrow or the day after.


End file.
